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Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
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Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Matarrese P, Signore M, Ascione B, Fanelli G, Paggi MG, Abbruzzese C. Chlorpromazine overcomes temozolomide resistance in glioblastoma by inhibiting Cx43 and essential DNA repair pathways. J Transl Med 2024; 22:667. [PMID: 39026284 PMCID: PMC11256652 DOI: 10.1186/s12967-024-05501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND In the fight against GBM, drug repurposing emerges as a viable and time-saving approach to explore new treatment options. Chlorpromazine, an old antipsychotic medication, has recently arisen as a promising candidate for repositioning in GBM therapy in addition to temozolomide, the first-line standard of care. We previously demonstrated the antitumor efficacy of chlorpromazine and its synergistic effects with temozolomide in suppressing GBM cell malignant features in vitro. This prompted us to accomplish a Phase II clinical trial to evaluate the efficacy and safety of adding chlorpromazine to temozolomide in GBM patients with unmethylated MGMT gene promoter. In this in vitro study, we investigate the potential role of chlorpromazine in overcoming temozolomide resistance. METHODS In our experimental set, we analyzed Connexin-43 expression at both the transcriptional and protein levels in control- and chlorpromazine-treated GBM cells. DNA damage and subsequent repair were assessed by immunofluorescence of γ-H2AX and Reverse-Phase Protein microArrays in chlorpromazine treated GBM cell lines. To elucidate the relationship between DNA repair systems and chemoresistance, we analyzed a signature of DNA repair genes in GBM cells after treatment with chlorpromazine, temozolomide and Connexin-43 downregulation. RESULTS Chlorpromazine treatment significantly downregulated connexin-43 expression in GBM cells, consequently compromising connexin-dependent cellular resilience, and ultimately contributing to cell death. In line with this, we observed concordant post-translational modifications of molecular determinants involved in DNA damage and repair pathways. Our evaluation of DNA repair genes revealed that temozolomide elicited an increase, while chlorpromazine, as well as connexin-43 silencing, a decrease in DNA repair gene expression in GBM cells. CONCLUSIONS Chlorpromazine potentiates the cytotoxic effects of the alkylating agent temozolomide through a mechanism involving downregulation of Cx43 expression and disruption of the cell cycle arrest essential for DNA repair processes. This finding suggests that chlorpromazine may be a potential therapeutic strategy to overcome TMZ resistance in GBM cells by inhibiting their DNA repair mechanisms.
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Affiliation(s)
- Paola Matarrese
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Michele Signore
- RPPA Unit, Proteomics Area, Core Facilities, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Barbara Ascione
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Giulia Fanelli
- Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Marco G Paggi
- Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - Claudia Abbruzzese
- Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
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Wang Z, Zhou X, Kong Q, He H, Sun J, Qiu W, Zhang L, Yang M. Extracellular Vesicle Preparation and Analysis: A State-of-the-Art Review. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401069. [PMID: 38874129 DOI: 10.1002/advs.202401069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/11/2024] [Indexed: 06/15/2024]
Abstract
In recent decades, research on Extracellular Vesicles (EVs) has gained prominence in the life sciences due to their critical roles in both health and disease states, offering promising applications in disease diagnosis, drug delivery, and therapy. However, their inherent heterogeneity and complex origins pose significant challenges to their preparation, analysis, and subsequent clinical application. This review is structured to provide an overview of the biogenesis, composition, and various sources of EVs, thereby laying the groundwork for a detailed discussion of contemporary techniques for their preparation and analysis. Particular focus is given to state-of-the-art technologies that employ both microfluidic and non-microfluidic platforms for EV processing. Furthermore, this discourse extends into innovative approaches that incorporate artificial intelligence and cutting-edge electrochemical sensors, with a particular emphasis on single EV analysis. This review proposes current challenges and outlines prospective avenues for future research. The objective is to motivate researchers to innovate and expand methods for the preparation and analysis of EVs, fully unlocking their biomedical potential.
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Affiliation(s)
- Zesheng Wang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Qinglong Kong
- The Second Department of Thoracic Surgery, Dalian Municipal Central Hospital, Dalian, 116033, P. R. China
| | - Huimin He
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Jiayu Sun
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Wenting Qiu
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Liang Zhang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Mengsu Yang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, 518000, P. R. China
- Department of Biomedical Sciences, and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, 999077, P. R. China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, P. R. China
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Ullah A, Chen Y, Singla RK, Cao D, Shen B. Pro-inflammatory cytokines and CXC chemokines as game-changer in age-associated prostate cancer and ovarian cancer: Insights from preclinical and clinical studies' outcomes. Pharmacol Res 2024; 204:107213. [PMID: 38750677 DOI: 10.1016/j.phrs.2024.107213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 06/01/2024]
Abstract
Prostate cancer (PC) and Ovarian cancer (OC) are two of the most common types of cancer that affect the reproductive systems of older men and women. These cancers are associated with a poor quality of life among the aged population. Therefore, finding new and innovative ways to detect, treat, and prevent these cancers in older patients is essential. Finding biomarkers for these malignancies will increase the chance of early detection and effective treatment, subsequently improving the survival rate. Studies have shown that the prevalence and health of some illnesses are linked to an impaired immune system. However, the age-associated changes in the immune system during malignancies such as PC and OC are poorly understood. Recent research has suggested that the excessive production of inflammatory immune mediators, such as interleukin-6 (IL-6), interleukin-8 (IL-8), transforming growth factor (TGF), tumor necrosis factor (TNF), CXC motif chemokine ligand 1 (CXCL1), CXC motif chemokine ligand 12 (CXCL12), and CXC motif chemokine ligand 13 (CXCL13), etc., significantly impact the development of PC and OC in elderly patients. Our review focuses on the latest functional studies of pro-inflammatory cytokines (interleukins) and CXC chemokines, which serve as biomarkers in elderly patients with PC and OC. Thus, we aim to shed light on how these biomarkers affect the development of PC and OC in elderly patients. We also examine the current status and future perspective of cytokines (interleukins) and CXC chemokines-based therapeutic targets in OC and PC treatment for elderly patients.
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Affiliation(s)
- Amin Ullah
- Department of Abdominal Oncology, Cancer Center of West China Hospital and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yongxiu Chen
- Gynecology Department, Guangdong Women and Children Hospital, No. 521, Xingnan Road, Panyu District, Guangzhou 511442, China
| | - Rajeev K Singla
- Department of Abdominal Oncology, Cancer Center of West China Hospital and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Dan Cao
- Department of Abdominal Oncology, Cancer Center of West China Hospital and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Bairong Shen
- Department of Abdominal Oncology, Cancer Center of West China Hospital and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
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Dhamdhere MR, Spiegelman VS. Extracellular vesicles in neuroblastoma: role in progression, resistance to therapy and diagnostics. Front Immunol 2024; 15:1385875. [PMID: 38660306 PMCID: PMC11041043 DOI: 10.3389/fimmu.2024.1385875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid pediatric cancer, and is one of the leading causes of cancer-related deaths in children. Despite the current multi-modal treatment regimens, majority of patients with advanced-stage NBs develop therapeutic resistance and relapse, leading to poor disease outcomes. There is a large body of knowledge on pathophysiological role of small extracellular vesicles (EVs) in progression and metastasis of multiple cancer types, however, the importance of EVs in NB was until recently not well understood. Studies emerging in the last few years have demonstrated the involvement of EVs in various aspects of NB pathogenesis. In this review we summarize these recent findings and advances on the role EVs play in NB progression, such as tumor growth, metastasis and therapeutic resistance, that could be helpful for future investigations in NB EV research. We also discuss different strategies for therapeutic targeting of NB-EVs as well as utilization of NB-EVs as potential biomarkers.
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Affiliation(s)
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, United States
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Samare-Najaf M, Kouchaki H, Moein Mahini S, Saberi Rounkian M, Tavakoli Y, Samareh A, Karim Azadbakht M, Jamali N. Prostate cancer: Novel genetic and immunologic biomarkers. Clin Chim Acta 2024; 555:117824. [PMID: 38316287 DOI: 10.1016/j.cca.2024.117824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024]
Abstract
Prostate cancer (PCa) is considered one of the most prevalent male malignancies worldwide with a global burden estimated to increase over the next two decades. Due to significant mortality and debilitation of survival, early diagnosis has been described as key. Unfortunately, current diagnostic serum-based strategies have low specificity and sensitivity. Histologic examination is invasive and not useful for treatment and monitoring purposes. Hence, a plethora of studies have been conducted to identify and validate an efficient noninvasive approach in the diagnosis, staging, and prognosis of PCa. These investigations may be categorized as genetic (non-coding biomarkers and gene markers), immunologic (immune cells, interleukins, cytokines, antibodies, and auto-antibodies), and heterogenous (PSA-related markers, PHI-related indices, and urinary biomarkers) subgroups. This review examines current approaches and potential strategies using biomarker panels in PCa.
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Affiliation(s)
- Mohammad Samare-Najaf
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Hosein Kouchaki
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Moein Mahini
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Masoumeh Saberi Rounkian
- Student Research Committee, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Yasaman Tavakoli
- Department of Medicine, Mazandaran University of Medical Sciences, Sari, Mazandaran, Iran
| | - Ali Samareh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Navid Jamali
- Department of Laboratory Sciences, Sirjan School of Medical Sciences, Sirjan, Iran.
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Saleh NA, Rode MP, Cisilotto J, Silva AH, Prigol AN, da Luz Efe F, Winter E, Filippin-Monteiro FB, Creczynski-Pasa TB. MicroRNA-Mediated Antiproliferative Effects of M1 Macrophage-Derived Extracellular Vesicles on Melanoma Cells. Immunol Invest 2024; 53:70-89. [PMID: 37981469 DOI: 10.1080/08820139.2023.2278774] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
INTRODUCTION Research in tumor treatment has shown promising results using extracellular vesicles (EVs) derived from immune cells. EVs derived from M1 macrophages (proinflammatory), known as M1-EVs, have properties that suppress tumor growth, making them a promising treatment tool for immune susceptible tumors such as melanoma. Here, small unaltered M1-EVs (M1-sEVs) were employed in a 3D mouse melanoma model (melanospheres) to evaluate such activity. METHODS Macrophages were polarized and EVs were isolated by ultracentrifugation. The EVs obtained were characterized based on size, with measurements performed by dynamic light scattering and electron microscopy, and the expression profiles of microRNAs were analyzed by microarray and PCR. Melanospheres were used to evaluate the cytotoxicity of M1-sEVs. Pondering a possible future transposition from the animal model to the human, human melanoma cells were transfected with a specific miRNA, and the impact on cell proliferation was evaluated. RESULTS The isolated EVs showed a size distribution between 50-400 nm in diameter, but preeminently in a range of 70-90 nm. M1-sEVs demonstrated a remarkable ability to reduce cell proliferation and viability in the melanospheres, leading to a decrease in their volume. M1-sEVs contained unique miRNAs, including miR-29a-3p, which exhibited significant antitumor activities according to bioinformatics analysis. Validation of the antitumor effects of miR-29a-3p was obtained by a functional evaluation, i.e., by inducing miRNA overexpression in human melanoma cells (SK-MEL-28). CONCLUSION Although further research would be advisable, the study provides evidence supporting the potential of M1-sEVs and their miRNA load as a possible targeted immune therapy for melanoma.
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Affiliation(s)
- Najla Adel Saleh
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Michele Patrícia Rode
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Júlia Cisilotto
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Adny Henrique Silva
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Anne Natalie Prigol
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Fernanda da Luz Efe
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Evelyn Winter
- Department of Agriculture, Biodiversity and Forest, Federal University of Santa Catarina, Curitibanos, Brazil
| | - Fabíola Branco Filippin-Monteiro
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
- Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Tânia Beatriz Creczynski-Pasa
- Postgraduate Program in Prharmacy, Federal University of Santa Catarina, Florianópolis, Brazil
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
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Samaržija I. The Potential of Extracellular Matrix- and Integrin Adhesion Complex-Related Molecules for Prostate Cancer Biomarker Discovery. Biomedicines 2023; 12:79. [PMID: 38255186 PMCID: PMC10813710 DOI: 10.3390/biomedicines12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/16/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Prostate cancer is among the top five cancer types according to incidence and mortality. One of the main obstacles in prostate cancer management is the inability to foresee its course, which ranges from slow growth throughout years that requires minimum or no intervention to highly aggressive disease that spreads quickly and resists treatment. Therefore, it is not surprising that numerous studies have attempted to find biomarkers of prostate cancer occurrence, risk stratification, therapy response, and patient outcome. However, only a few prostate cancer biomarkers are used in clinics, which shows how difficult it is to find a novel biomarker. Cell adhesion to the extracellular matrix (ECM) through integrins is among the essential processes that govern its fate. Upon activation and ligation, integrins form multi-protein intracellular structures called integrin adhesion complexes (IACs). In this review article, the focus is put on the biomarker potential of the ECM- and IAC-related molecules stemming from both body fluids and prostate cancer tissue. The processes that they are involved in, such as tumor stiffening, bone turnover, and communication via exosomes, and their biomarker potential are also reviewed.
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Affiliation(s)
- Ivana Samaržija
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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Abbruzzese C, Matteoni S, Matarrese P, Signore M, Ascione B, Iessi E, Gurtner A, Sacconi A, Ricci-Vitiani L, Pallini R, Pace A, Villani V, Polo A, Costantini S, Budillon A, Ciliberto G, Paggi MG. Chlorpromazine affects glioblastoma bioenergetics by interfering with pyruvate kinase M2. Cell Death Dis 2023; 14:821. [PMID: 38092755 PMCID: PMC10719363 DOI: 10.1038/s41419-023-06353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Glioblastoma (GBM) is the most frequent and lethal brain tumor, whose therapeutic outcome - only partially effective with current schemes - places this disease among the unmet medical needs, and effective therapeutic approaches are urgently required. In our attempts to identify repositionable drugs in glioblastoma therapy, we identified the neuroleptic drug chlorpromazine (CPZ) as a very promising compound. Here we aimed to further unveil the mode of action of this drug. We performed a supervised recognition of the signal transduction pathways potentially influenced by CPZ via Reverse-Phase Protein microArrays (RPPA) and carried out an Activity-Based Protein Profiling (ABPP) followed by Mass Spectrometry (MS) analysis to possibly identify cellular factors targeted by the drug. Indeed, the glycolytic enzyme PKM2 was identified as one of the major targets of CPZ. Furthermore, using the Seahorse platform, we analyzed the bioenergetics changes induced by the drug. Consistent with the ability of CPZ to target PKM2, we detected relevant changes in GBM energy metabolism, possibly attributable to the drug's ability to inhibit the oncogenic properties of PKM2. RPE-1 non-cancer neuroepithelial cells appeared less responsive to the drug. PKM2 silencing reduced the effects of CPZ. 3D modeling showed that CPZ interacts with PKM2 tetramer in the same region involved in binding other known activators. The effect of CPZ can be epitomized as an inhibition of the Warburg effect and thus malignancy in GBM cells, while sparing RPE-1 cells. These preclinical data enforce the rationale that allowed us to investigate the role of CPZ in GBM treatment in a recent multicenter Phase II clinical trial.
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Affiliation(s)
- Claudia Abbruzzese
- Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS - Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Silvia Matteoni
- Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS - Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Paola Matarrese
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Michele Signore
- RPPA Unit, Proteomics Area, Core Facilities, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Barbara Ascione
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Elisabetta Iessi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Aymone Gurtner
- SAFU Unit, IRCCS - Regina Elena National Cancer Institute, 00144, Rome, Italy
- The Institute of Translational Pharmacology - IFT - CNR, Rome, Italy
| | - Andrea Sacconi
- UOSD Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS - Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Roberto Pallini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Institute of Neurosurgery, Catholic University School of Medicine, 00168, Rome, Italy
| | - Andrea Pace
- Neuro-Oncology, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Veronica Villani
- Neuro-Oncology, IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | - Andrea Polo
- Experimental Pharmacology Unit, Laboratori di Mercogliano, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Napoli, Italy
| | - Susan Costantini
- Experimental Pharmacology Unit, Laboratori di Mercogliano, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Napoli, Italy
| | - Alfredo Budillon
- Scientific Directorate, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Napoli, Italy
| | - Gennaro Ciliberto
- Scientific Directorate, IRCCS - Regina Elena National Cancer Institute, 00144, Rome, Italy
| | - Marco G Paggi
- Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS - Regina Elena National Cancer Institute, 00144, Rome, Italy.
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Asleh K, Dery V, Taylor C, Davey M, Djeungoue-Petga MA, Ouellette RJ. Extracellular vesicle-based liquid biopsy biomarkers and their application in precision immuno-oncology. Biomark Res 2023; 11:99. [PMID: 37978566 PMCID: PMC10655470 DOI: 10.1186/s40364-023-00540-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
While the field of precision oncology is rapidly expanding and more targeted options are revolutionizing cancer treatment paradigms, therapeutic resistance particularly to immunotherapy remains a pressing challenge. This can be largely attributed to the dynamic tumor-stroma interactions that continuously alter the microenvironment. While to date most advancements have been made through examining the clinical utility of tissue-based biomarkers, their invasive nature and lack of a holistic representation of the evolving disease in a real-time manner could result in suboptimal treatment decisions. Thus, using minimally-invasive approaches to identify biomarkers that predict and monitor treatment response as well as alert to the emergence of recurrences is of a critical need. Currently, research efforts are shifting towards developing liquid biopsy-based biomarkers obtained from patients over the course of disease. Liquid biopsy represents a unique opportunity to monitor intercellular communication within the tumor microenvironment which could occur through the exchange of extracellular vesicles (EVs). EVs are lipid bilayer membrane nanoscale vesicles which transfer a plethora of biomolecules that mediate intercellular crosstalk, shape the tumor microenvironment, and modify drug response. The capture of EVs using innovative approaches, such as microfluidics, magnetic beads, and aptamers, allow their analysis via high throughput multi-omics techniques and facilitate their use for biomarker discovery. Artificial intelligence, using machine and deep learning algorithms, is advancing multi-omics analyses to uncover candidate biomarkers and predictive signatures that are key for translation into clinical trials. With the increasing recognition of the role of EVs in mediating immune evasion and as a valuable biomarker source, these real-time snapshots of cellular communication are promising to become an important tool in the field of precision oncology and spur the recognition of strategies to block resistance to immunotherapy. In this review, we discuss the emerging role of EVs in biomarker research describing current advances in their isolation and analysis techniques as well as their function as mediators in the tumor microenvironment. We also highlight recent lung cancer and melanoma studies that point towards their application as predictive biomarkers for immunotherapy and their potential clinical use in precision immuno-oncology.
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Affiliation(s)
- Karama Asleh
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada.
| | - Valerie Dery
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, New Brunswick, Canada
| | - Catherine Taylor
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Michelle Davey
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | | | - Rodney J Ouellette
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, New Brunswick, Canada
- Dr Georges L. Dumont University Hospital, Vitalite Health Network, Moncton, New Brunswick, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
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11
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Zhang J, Guan M, Lv M, Liu Y, Zhang H, Zhang Z, Zhang K. Localized Imaging of Programmed Death-Ligand 1 on Individual Tumor-Derived Extracellular Vesicles for Prediction of Immunotherapy Response. ACS NANO 2023; 17:20120-20134. [PMID: 37819165 DOI: 10.1021/acsnano.3c05799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Programmed death-ligand 1 (PD-L1) on tumor-derived small extracellular vesicles (EVs) is a biomarker for prediction of the immunotherapy response. However, conventional bulk measurement can hardly analyze the expression of PD-L1 on individual tumor-derived EVs. Herein, a method for localized imaging of tumor-derived individual EVs PD-L1 (LITIE) is developed. In this assay, EVs in plasma were directly captured on a biochip. Then the liposome-mediated membrane fusion strategy was used to image miR-21 in EVs to discriminate miR-21-positive EVs from the whole EVs populations. Subsequently, the primer exchange reaction (PER) is applied to generate localized and amplified fluorescent signals for imaging PD-L1 on identified tumor-derived EVs. When applied in clinical sample tests, the LITIE assay could effectively distinguish breast cancer patients from healthy donors or patients with benign tumors. Interestingly, in a mice melanoma model, the LITIE assay showed the ability to predict immunotherapy response even before drug treatment. Thus, we think the strategy of measuring individual tumor-derived EVs PD-L1 could serve as an alternative way for screening clinical responders suitable for immunotherapy.
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Affiliation(s)
- Junli Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China
| | - Mengting Guan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min Lv
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yingying Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Hongling Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China
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Abstract
ABSTRACT The advent of high-throughput technologies has enabled the analysis of minute amounts of tumor-derived material purified from body fluids, termed "liquid biopsies." Prostate cancer (PCa) management, like in many other cancer types, has benefited from liquid biopsies at several stages of the disease. Although initially describing circulating tumor cells in blood, the term "liquid biopsy" has come to more prominently include cell-free, circulating tumor DNA, as well as RNA, proteins, and other molecules. They provide tumor molecular information representing the entire, often-heterogeneous disease, relatively noninvasively and longitudinally. Blood has been the main liquid biopsy specimen in PCa, and urine has also proven beneficial. Technological advances have allowed clinical implementation of some liquid biopsies in PCa, in disease monitoring and precision oncology. This narrative review introduces the main types of blood-based PCa liquid biopsies focusing on advances in the past 5 years. Clinical adoption of liquid biopsies to detect and monitor the evolving PCa tumor biology promises to deepen our understanding of the disease and improve patient outcomes.
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Affiliation(s)
- Andi K. Cani
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Simpa S. Salami
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
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13
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Chen L, Ou Q, Kou X. Extracellular vesicles and their indispensable roles in pathogenesis and treatment of inflammatory bowel disease: A comprehensive review. Life Sci 2023; 327:121830. [PMID: 37286163 DOI: 10.1016/j.lfs.2023.121830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Inflammatory bowel disease (IBD) is a global disease with rising incidence worldwide, and its debilitating symptoms and dissatisfactory therapies have brought heavy burdens for patients. Extracellular vesicles (EVs), a heterogeneous population of lipid bilayer membranes containing abundant bioactive molecules, have been indicated to play important roles in the pathogenesis and treatment of many diseases. However, to our knowledge, comprehensive reviews summarizing the various roles of diverse source-derived EVs in the pathogenesis and treatment of IBD are still lacking. This review, not only summarizes the EV characteristics, but also focuses on the multiple roles of diverse EVs in IBD pathogenesis and their treatment potential. In addition, hoping to push forward the research frontiers, we point out several challenges that the researchers are faced, about EVs in current IBD research and future therapeutic applications. We also put forward our prospects on future exploration regarding EVs in IBD treatment, including developing IBD vaccines and paying more attention on apoptotic vesicles. This review is aimed to enrich the knowledge on the indispensable roles of EVs in IBD pathogenesis and treatment, providing ideas and reference for future therapeutic strategy for IBD treatment.
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Affiliation(s)
- Linling Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, 510055 Guangzhou, China
| | - Qianmin Ou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, 510055 Guangzhou, China
| | - Xiaoxing Kou
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, 510055 Guangzhou, China; Key Laboratory of Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510055, China.
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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15
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Bertani G, Di Tinco R, Bertoni L, Orlandi G, Pisciotta A, Rosa R, Rigamonti L, Signore M, Bertacchini J, Sena P, De Biasi S, Villa E, Carnevale G. Flow-dependent shear stress affects the biological properties of pericyte-like cells isolated from human dental pulp. Stem Cell Res Ther 2023; 14:31. [PMID: 36805780 PMCID: PMC9938980 DOI: 10.1186/s13287-023-03254-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/12/2023] [Indexed: 02/20/2023] Open
Abstract
BACKGROUND Human dental pulp stem cells represent a mesenchymal stem cell niche localized in the perivascular area of dental pulp and are characterized by low immunogenicity and immunomodulatory/anti-inflammatory properties. Pericytes, mural cells surrounding the endothelium of small vessels, regulate numerous functions including vessel growth, stabilization and permeability. It is well established that pericytes have a tight cross talk with endothelial cells in neoangiogenesis and vessel stabilization, which are regulated by different factors, i.e., microenvironment and flow-dependent shear stress. The aim of this study was to evaluate the effects of a pulsatile unidirectional flow in the presence or not of an inflammatory microenvironment on the biological properties of pericyte-like cells isolated from human dental pulp (hDPSCs). METHODS Human DPSCs were cultured under both static and dynamic conditions with or without pre-activated peripheral blood mononuclear cells (PBMCs). Pulsatile unidirectional flow shear stress was generated by using a specific peristaltic pump. The angiogenic potential and inflammatory properties of hDPSCs were evaluated through reverse phase protein microarrays (RPPA), confocal immunofluorescence and western blot analyses. RESULTS Our data showed that hDPSCs expressed the typical endothelial markers, which were up-regulated after endothelial induction, and were able to form tube-like structures. RPPA analyses revealed that these properties were modulated when a pulsatile unidirectional flow shear stress was applied to hDPSCs. Stem cells also revealed a downregulation of the immune-modulatory molecule PD-L1, in parallel with an up-regulation of the pro-inflammatory molecule NF-kB. Immune-modulatory properties of hDPSCs were also reduced after culture under flow-dependent shear stress and exposure to an inflammatory microenvironment. This evidence was strengthened by the detection of up-regulated levels of expression of pro-inflammatory cytokines in PBMCs. CONCLUSIONS In conclusion, the application of a pulsatile unidirectional flow shear stress induced a modulation of immunomodulatory/inflammatory properties of dental pulp pericyte-like cells.
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Affiliation(s)
- Giulia Bertani
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Rosanna Di Tinco
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura Bertoni
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Orlandi
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandra Pisciotta
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberto Rosa
- grid.7548.e0000000121697570Department of Engineering Sciences and Methods, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Rigamonti
- grid.7548.e0000000121697570Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Michele Signore
- grid.416651.10000 0000 9120 6856RPPA Unit, Proteomics Area, Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Jessika Bertacchini
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Paola Sena
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Sara De Biasi
- grid.7548.e0000000121697570Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Erica Villa
- grid.7548.e0000000121697570Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy
| | - Gianluca Carnevale
- Department of Surgery, Medicine Dentistry and Morphological Sciences With Interest in Transplant, University of Modena and Reggio Emilia, Modena, Italy.
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16
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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Shaba E, Vantaggiato L, Governini L, Haxhiu A, Sebastiani G, Fignani D, Grieco GE, Bergantini L, Bini L, Landi C. Multi-Omics Integrative Approach of Extracellular Vesicles: A Future Challenging Milestone. Proteomes 2022; 10:proteomes10020012. [PMID: 35645370 PMCID: PMC9149947 DOI: 10.3390/proteomes10020012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
In the era of multi-omic sciences, dogma on singular cause-effect in physio-pathological processes is overcome and system biology approaches have been providing new perspectives to see through. In this context, extracellular vesicles (EVs) are offering a new level of complexity, given their role in cellular communication and their activity as mediators of specific signals to target cells or tissues. Indeed, their heterogeneity in terms of content, function, origin and potentiality contribute to the cross-interaction of almost every molecular process occurring in a complex system. Such features make EVs proper biological systems being, therefore, optimal targets of omic sciences. Currently, most studies focus on dissecting EVs content in order to either characterize it or to explore its role in various pathogenic processes at transcriptomic, proteomic, metabolomic, lipidomic and genomic levels. Despite valuable results being provided by individual omic studies, the categorization of EVs biological data might represent a limit to be overcome. For this reason, a multi-omic integrative approach might contribute to explore EVs function, their tissue-specific origin and their potentiality. This review summarizes the state-of-the-art of EVs omic studies, addressing recent research on the integration of EVs multi-level biological data and challenging developments in EVs origin.
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Affiliation(s)
- Enxhi Shaba
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
- Correspondence:
| | - Lorenza Vantaggiato
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
| | - Laura Governini
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (L.G.); (A.H.)
| | - Alesandro Haxhiu
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (L.G.); (A.H.)
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Daniela Fignani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Giuseppina Emanuela Grieco
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; (G.S.); (D.F.); (G.E.G.)
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences, 53100 Siena, Italy
| | - Laura Bergantini
- Respiratory Diseases and Lung Transplant Unit, Department of Medical Sciences, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy;
| | - Luca Bini
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
| | - Claudia Landi
- Functional Proteomics Lab, Department of Life Sciences, University of Siena, 53100 Siena, Italy; (L.V.); (L.B.); (C.L.)
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Rodrigues-Junior DM, Tsirigoti C, Lim SK, Heldin CH, Moustakas A. Extracellular Vesicles and Transforming Growth Factor β Signaling in Cancer. Front Cell Dev Biol 2022; 10:849938. [PMID: 35493080 PMCID: PMC9043557 DOI: 10.3389/fcell.2022.849938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
Complexity in mechanisms that drive cancer development and progression is exemplified by the transforming growth factor β (TGF-β) signaling pathway, which suppresses early-stage hyperplasia, yet assists aggressive tumors to achieve metastasis. Of note, several molecules, including mRNAs, non-coding RNAs, and proteins known to be associated with the TGF-β pathway have been reported as constituents in the cargo of extracellular vesicles (EVs). EVs are secreted vesicles delimited by a lipid bilayer and play critical functions in intercellular communication, including regulation of the tumor microenvironment and cancer development. Thus, this review aims at summarizing the impact of EVs on TGF-β signaling by focusing on mechanisms by which EV cargo can influence tumorigenesis, metastatic spread, immune evasion and response to anti-cancer treatment. Moreover, we emphasize the potential of TGF-β-related molecules present in circulating EVs as useful biomarkers of prognosis, diagnosis, and prediction of response to treatment in cancer patients.
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Affiliation(s)
| | - Chrysoula Tsirigoti
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sai Kiang Lim
- Institute of Molecular and Cell Biology (A*-STAR), Singapore, Singapore
| | - Carl-Henrik Heldin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- *Correspondence: Aristidis Moustakas,
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Abstract
Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case in cancer liquid biopsies, deep proteome profiling will likely provide invaluable and clinically relevant information in real-time throughout all stages of cancer progression. However, due to the great complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies, proteomic discoveries have yet lagged behind their counterpart, genomic technologies. Therefore, novel protein technologies are in urgent demand to fulfill the goals set out for biomarker discovery in cancer liquid biopsies.Notably, conventional and innovative technologies are being rapidly developed for proteomic analysis in cancer liquid biopsies. These advances have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution, adapted or adopted in response to therapeutic interventions. In this paper, we review the high-plex proteomics technologies that are capable of measuring at least hundreds of proteins simultaneously from liquid biopsy samples, ranging from traditional technologies based on mass spectrometry (MS) and antibody/antigen arrays to innovative technologies based on aptamer, proximity extension assay (PEA), and reverse phase protein arrays (RPPA).
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20
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Samami E, Pourali G, Arabpour M, Fanipakdel A, Shahidsales S, Javadinia SA, Hassanian SM, Mohammadparast S, Avan A. The Potential Diagnostic and Prognostic Value of Circulating MicroRNAs in the Assessment of Patients With Prostate Cancer: Rational and Progress. Front Oncol 2022; 11:716831. [PMID: 35186706 PMCID: PMC8855122 DOI: 10.3389/fonc.2021.716831] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 12/31/2021] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer (P.C.) is one of the most frequent diagnosed cancers among men and the first leading cause of death with an annual incidence of 1.4 million worldwide. Prostate-specific antigen is being used for screening/diagnosis of prostate disease, although it is associated with several limitations. Thus, identification of novel biomarkers is warranted for diagnosis of patients at earlier stages. MicroRNAs (miRNAs) are recently being emerged as potential biomarkers. It has been shown that these small molecules can be circulated in body fluids and prognosticate the risk of developing P.C. Several miRNAs, including MiR-20a, MiR-21, miR-375, miR-378, and miR-141, have been proposed to be expressed in prostate cancer. This review summarizes the current knowledge about possible molecular mechanisms and potential application of tissue specific and circulating microRNAs as diagnosis, prognosis, and therapeutic targets in prostate cancer.
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Affiliation(s)
- Elham Samami
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazaleh Pourali
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahla Arabpour
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azar Fanipakdel
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Seyed Alireza Javadinia
- Vasei Clinical Research Development Unit, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeid Mohammadparast
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- *Correspondence: Amir Avan,
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21
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Signore M, Manganelli V. Reverse Phase Protein Arrays in cancer stem cells. Methods Cell Biol 2022; 171:33-61. [DOI: 10.1016/bs.mcb.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Basu B, Karmakar S. The Role of Extracellular Vesicles in the Progression of Tumors towards Metastasis. Physiology (Bethesda) 2021. [DOI: 10.5772/intechopen.101635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Extracellular vesicles (EVs) are cell-derived lipid membrane bound vesicles that serve as mediators of intercellular communication. EVs have been found to regulate a wide range of cellular processes through the transference of genetic, protein and lipid messages from the host cell to the recipient cell. Unsurprisingly, this major mode of intracellular communication would be abrogated in cancer. Ever increasing evidence points towards a key role of EVs in promoting tumor development and in contributing to the various stages of metastasis. Tumor released EVs have been shown to facilitate the transference of oncogenic proteins and nucleic acids to other tumor cells and to the surrounding stromal cells, thereby setting up a tumor permissive microenvironment. EVs released from tumor cells have been shown to promote extracellular matrix (ECM) remodeling through the modulation of neighboring tumor cells and stromal cells. EVs released from disseminated tumor cells have been reported to attract circulating tumor cells (CTCs) via chemotaxis and induce the production of specific extracellular matrix components from neighboring stromal cells so as to support the growth of metastatic cells at the secondary tumor site. Circulating levels of tumor derived EVs of patients have been correlated with incidence of metastasis and disease relapse.
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Yan Y, Yeon SY, Qian C, You S, Yang W. On the Road to Accurate Protein Biomarkers in Prostate Cancer Diagnosis and Prognosis: Current Status and Future Advances. Int J Mol Sci 2021; 22:13537. [PMID: 34948334 PMCID: PMC8703658 DOI: 10.3390/ijms222413537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/14/2021] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PC) is a leading cause of morbidity and mortality among men worldwide. Molecular biomarkers work in conjunction with existing clinicopathologic tools to help physicians decide who to biopsy, re-biopsy, treat, or re-treat. The past decade has witnessed the commercialization of multiple PC protein biomarkers with improved performance, remarkable progress in proteomic technologies for global discovery and targeted validation of novel protein biomarkers from clinical specimens, and the emergence of novel, promising PC protein biomarkers. In this review, we summarize these advances and discuss the challenges and potential solutions for identifying and validating clinically useful protein biomarkers in PC diagnosis and prognosis. The identification of multi-protein biomarkers with high sensitivity and specificity, as well as their integration with clinicopathologic parameters, imaging, and other molecular biomarkers, bodes well for optimal personalized management of PC patients.
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Affiliation(s)
- Yiwu Yan
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (Y.Y.); (S.Y.Y.); (C.Q.); (S.Y.)
| | - Su Yeon Yeon
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (Y.Y.); (S.Y.Y.); (C.Q.); (S.Y.)
| | - Chen Qian
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (Y.Y.); (S.Y.Y.); (C.Q.); (S.Y.)
| | - Sungyong You
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (Y.Y.); (S.Y.Y.); (C.Q.); (S.Y.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wei Yang
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (Y.Y.); (S.Y.Y.); (C.Q.); (S.Y.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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Ganini C, Amelio I, Bertolo R, Candi E, Cappello A, Cipriani C, Mauriello A, Marani C, Melino G, Montanaro M, Natale ME, Tisone G, Shi Y, Wang Y, Bove P. Serine and one-carbon metabolisms bring new therapeutic venues in prostate cancer. Discov Oncol 2021; 12:45. [PMID: 35201488 PMCID: PMC8777499 DOI: 10.1007/s12672-021-00440-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022] Open
Abstract
Serine and one-carbon unit metabolisms are essential biochemical pathways implicated in fundamental cellular functions such as proliferation, biosynthesis of important anabolic precursors and in general for the availability of methyl groups. These two distinct but interacting pathways are now becoming crucial in cancer, the de novo cytosolic serine pathway and the mitochondrial one-carbon metabolism. Apart from their role in physiological conditions, such as epithelial proliferation, the serine metabolism alterations are associated to several highly neoplastic proliferative pathologies. Accordingly, prostate cancer shows a deep rearrangement of its metabolism, driven by the dependency from the androgenic stimulus. Several new experimental evidence describes the role of a few of the enzymes involved in the serine metabolism in prostate cancer pathogenesis. The aim of this study is to analyze gene and protein expression data publicly available from large cancer specimens dataset, in order to further dissect the potential role of the abovementioned metabolism in the complex reshaping of the anabolic environment in this kind of neoplasm. The data suggest a potential role as biomarkers as well as in cancer therapy for the genes (and enzymes) belonging to the one-carbon metabolism in the context of prostatic cancer.
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Affiliation(s)
- Carlo Ganini
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- IDI-IRCCS, Rome, Italy
| | - Ivano Amelio
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
| | - Riccardo Bertolo
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- IDI-IRCCS, Rome, Italy
| | - Angela Cappello
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- IDI-IRCCS, Rome, Italy
| | - Chiara Cipriani
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
| | - Carla Marani
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
| | - Manuela Montanaro
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
| | - Maria Emanuela Natale
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - Giuseppe Tisone
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
| | - Yufang Shi
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031 China
- The First Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, 199 Renai Road, Suzhou, 215123 Jiangsu China
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031 China
| | - Pierluigi Bove
- Department of Experimental Medicine, Torvergata Oncoscience Research Centre of Excellence, TOR, University of Rome Tor Vergata, a Montpellier 1, 00133 Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
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